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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ), 'gf_id' => 'HOM05D001259', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001259' ), 'data_identifier' => 'HOM05D001259', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001259', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22130' => 'bna', 'A03p42330' => 'bna', 'A03p64000' => 'bna', 'A04p08670' => 'bna', 'A05p27130' => 'bna', 'A06p33570' => 'bna', 'A07p03100' => 'bna', 'A09p44260' => 'bna', 'Aa31LG4G19280' => 'aar', 'Aa31LG6G12950' => 'aar', 'Aa31LG8G15060' => 'aar', 'Aa31LG8G8260' => 'aar', 'Aa31LG9G1990' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2856' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.211' => 'aag', 'Actinidia00617' => 'ach', 'Actinidia07453' => 'ach', 'Actinidia17429' => 'ach', 'Actinidia20507' => 'ach', 'Actinidia22960' => 'ach', 'Actinidia26541' => 'ach', 'Actinidia32653' => 'ach', 'Ah.01g008530' => 'amhyb', 'AL3G35710' => 'aly', 'AL3G35720' => 'aly', 'AL3G50870' => 'aly', 'AL5G31650' => 'aly', 'AL7G15060' => 'aly', 'AL7G40100' => 'aly', 'Aqoxy5G01814' => 'aox', 'Aqoxy6G02187' => 'aox', 'arahy.Tifrunner.gnm1.ann1.13R07Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3V4UGK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.436L1R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H6MCI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8M9DZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E41BXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVW9RW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHLG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KXY93B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS4NYU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VH3KGW' => 'arhy', 'AT2G17840' => 'ath', 'AT3G21590' => 'ath', 'AT3G21600' => 'ath', 'AT3G51250' => 'ath', 'AT4G15450' => 'ath', 'AT4G35985' => 'ath', 'ATR0705G005' => 'atr', 'ATR0705G096' => 'atr', 'ATR0712G002' => 'atr', 'Atru.chr3.839' => 'acertr', 'Atru.chr5.3299' => 'acertr', 'Atru.chr5.3300' => 'acertr', 'Atru.chr7.1461' => 'acertr', 'Atru.chr7.1462' => 'acertr', 'AUR62003351' => 'cqu', 'AUR62010055' => 'cqu', 'AUR62010915' => 'cqu', 'AUR62013047' => 'cqu', 'AUR62021411' => 'cqu', 'AUR62029485' => 'cqu', 'BcaB01g00538' => 'bca', 'BcaB01g00707' => 'bca', 'BcaB03g16557' => 'bca', 'BcaB06g26265' => 'bca', 'BcaB06g27919' => 'bca', 'BcaB08g34769' => 'bca', 'BcaC01g02883' => 'bca', 'BcaC01g03497' => 'bca', 'BcaC05g28153' => 'bca', 'BcaC06g36334' => 'bca', 'BcaC09g50235' => 'bca', 'BcaNung00274' => 'bca', 'BcaNung05049' => 'bca', 'BcaNung05050' => 'bca', 'BolC1t02691H' => 'bol', 'BolC2t08723H' => 'bol', 'BolC3t17463H' => 'bol', 'BolC3t18134H' => 'bol', 'BolC5t32920H' => 'bol', 'BolC7t40923H' => 'bol', 'BolC7t46571H' => 'bol', 'BolC8t50266H' => 'bol', 'BraA01t02122Z' => 'bra', 'BraA03t13385Z' => 'bra', 'BraA03t15467Z' => 'bra', 'BraA05t21599Z' => 'bra', 'BraA06t26294Z' => 'bra', 'BraA06t27397Z' => 'bra', 'BraA07t28108Z' => 'bra', 'BraA09t39888Z' => 'bra', 'C01p27630' => 'bna', 'C03p51790' => 'bna', 'C03p58770' => 'bna', 'C05p41870' => 'bna', 'C07p05250' => 'bna', 'C07p61460' => 'bna', 'C08p26520' => 'bna', 'CAN.G1241.32' => 'can', 'CAN.G1274.22' => 'can', 'CAN.G1485.1' => 'can', 'CAN.G3392.1' => 'can', 'CAN.G588.63' => 'can', 'CANSAT25G2159' => 'cansat', 'CANSAT25G3287' => 'cansat', 'CANSAT56G1287' => 'cansat', 'CANSAT56G3268' => 'cansat', 'CANSAT56G3717' => 'cansat', 'CARHR097550' => 'chi', 'CARHR097570' => 'chi', 'CARHR108340' => 'chi', 'CARHR160830' => 'chi', 'CARHR222210' => 'chi', 'CARHR244370' => 'chi', 'Carub.0003s2163' => 'cru', 'Carub.0003s2164' => 'cru', 'Carub.0003s3198' => 'cru', 'Carub.0005s1762' => 'cru', 'Carub.0007s0424' => 'cru', 'Carub.0007s2646' => 'cru', 'Ca_19059_v3' => 'car', 'Ca_22391_v3' => 'car', 'Ca_24915_v3' => 'car', 'Ca_25570_v3' => 'car', 'CBR_g10814' => 'cbr', 'Cc06_g10450' => 'ccan', 'Cc07_g10980' => 'ccan', 'Cc11_g15200' => 'ccan', 'CDE05G0198' => 'cde', 'CDE05G2810' => 'cde', 'CDE05G3309' => 'cde', 'Cfa003183' => 'cfa', 'Cfa005229' => 'cfa', 'Cfa005528' => 'cfa', 'Cfa006991' => 'cfa', 'Cfa007068' => 'cfa', 'Ciclev10008680m.g' => 'ccl', 'Ciclev10025594m.g' => 'ccl', 'Ciclev10028214m.g' => 'ccl', 'CiPaw.04G158100' => 'cil', 'CiPaw.04G158200' => 'cil', 'CiPaw.05G080700' => 'cil', 'CiPaw.07G060400' => 'cil', 'CiPaw.08G129600' => 'cil', 'ClCG02G011850' => 'cla', 'ClCG03G016160' => 'cla', 'ClCG10G000630' => 'cla', 'COL.COLO4_16704' => 'col', 'COL.COLO4_17315' => 'col', 'COL.COLO4_22450' => 'col', 'COL.COLO4_34746' => 'col', 'Cpa.g.sc37.152' => 'cpa', 'Cpa.g.sc40.98' => 'cpa', 'Cpa.g.sc40.99' => 'cpa', 'Cpa.g.sc6.276' => 'cpa', 'Cre04.g217930' => 'cre', 'CsaV3_1G039770' => 'csa', 'CsaV3_2G016000' => 'csa', 'CsaV3_3G000710' => 'csa', 'CSS0005097' => 'camsi', 'CSS0007335' => 'camsi', 'CSS0008651' => 'camsi', 'CSS0008740' => 'camsi', 'CSS0016558' => 'camsi', 'CSS0021309' => 'camsi', 'CSS0037025' => 'camsi', 'CSS0037971' => 'camsi', 'CSS0038801' => 'camsi', 'CSS0048627' => 'camsi', 'DCAR_003162' => 'dca', 'DCAR_010145' => 'dca', 'DCAR_010690' => 'dca', 'Dinv14094' => 'din', 'Dinv36689' => 'din', 'Dinv40108' => 'din', 'Dinv41665' => 'din', 'Duzib132G0120' => 'dzi', 'Duzib147G0435' => 'dzi', 'Duzib168G0295' => 'dzi', 'ECA232G2801' => 'eca', 'ECA233G3361' => 'eca', 'ECA240G0832' => 'eca', 'ECA240G1616' => 'eca', 'EL10Ac6g15492' => 'bvu', 'EL10Ac8g18382' => 'bvu', 'EL10Ac9g21395' => 'bvu', 'Eucgr.C00998' => 'egr', 'Eucgr.I01404' => 'egr', 'Eucgr.I02336' => 'egr', 'Eucgr.L02525' => 'egr', 'FAN19G1600' => 'fan', 'FAN19G1704' => 'fan', 'FAN20G3135' => 'fan', 'FAN23G1183' => 'fan', 'FAN24G0964' => 'fan', 'FAN26G2129' => 'fan', 'FAN27G3341' => 'fan', 'FAN28G0868' => 'fan', 'FAN28G1996' => 'fan', 'FvH4_1g06090' => 'fve', 'FvH4_1g11540' => 'fve', 'FvH4_2g01340' => 'fve', 'Glyma.01G008100' => 'gma', 'Glyma.01G164900' => 'gma', 'Glyma.02G046700' => 'gma', 'Glyma.05G226900' => 'gma', 'Glyma.08G033700' => 'gma', 'Glyma.11G078200' => 'gma', 'Glyma.11G106900' => 'gma', 'Glyma.12G031900' => 'gma', 'Glyma.16G078200' => 'gma', 'Glyma.16G125000' => 'gma', 'Gohir.A02G171800' => 'ghi', 'Gohir.A06G067100' => 'ghi', 'Gohir.A08G243000' => 'ghi', 'Gohir.A12G037800' => 'ghi', 'Gohir.D03G008300' => 'ghi', 'Gohir.D06G065700' => 'ghi', 'Gohir.D08G263900' => 'ghi', 'Gohir.D12G034600' => 'ghi', 'Gorai.003G008500' => 'gra', 'Gorai.004G281800' => 'gra', 'Gorai.008G035600' => 'gra', 'Gorai.010G077000' => 'gra', 'GSVIVG01015304001' => 'vvi', 'GSVIVG01018750001' => 'vvi', 'GSVIVG01024039001' => 'vvi', 'HanXRQChr03g0061201' => 'han', 'HanXRQChr09g0256731' => 'han', 'HanXRQChr15g0478811' => 'han', 'HanXRQChr17g0557651' => 'han', 'Haze_02155' => 'cav', 'Haze_03740' => 'cav', 'Hma1.2p1_0012F.1_g007350' => 'hma', 'Hma1.2p1_0869F.1_g230770' => 'hma', 'HPP92_022175' => 'vpl', 'HPP92_022748' => 'vpl', 'HPP92_022970' => 'vpl', 'Hund00029' => 'sun', 'Hund09111' => 'sun', 'Hund14056' => 'sun', 'Hund16499' => 'sun', 'Lalb_Chr03g0025101' => 'lal', 'Lalb_Chr05g0212321' => 'lal', 'Lalb_Chr05g0223221' => 'lal', 'Lalb_Chr16g0391351' => 'lal', 'Lalb_Chr24g0397321' => 'lal', 'Lj2C479G9' => 'lonja', 'Lj2g0006993' => 'lja', 'Lj2g0015337' => 'lja', 'Lj3g0013829' => 'lja', 'Lj4C221G10' => 'lonja', 'Lj4g0011285' => 'lja', 'Lj4g0018158' => 'lja', 'Lj5A181T52' => 'lonja', 'Lj5A181T53' => 'lonja', 'Lj7A665T29' => 'lonja', 'Lj7C665T5' => 'lonja', 'Lsat_1_v5_gn_1_128180' => 'lsa', 'Lsat_1_v5_gn_2_18200' => 'lsa', 'Lsat_1_v5_gn_3_104461' => 'lsa', 'Lsat_1_v5_gn_3_127420' => 'lsa', 'Lsat_1_v5_gn_3_46320' => 'lsa', 'Lsat_1_v5_gn_4_145861' => 'lsa', 'Lsat_1_v5_gn_4_185261' => 'lsa', 'Lsat_1_v5_gn_5_106780' => 'lsa', 'Lsat_1_v5_gn_5_147721' => 'lsa', 'Lsat_1_v5_gn_7_30101' => 'lsa', 'Lsat_1_v5_gn_7_30121' => 'lsa', 'Lsat_1_v5_gn_7_39781' => 'lsa', 'Lsat_1_v5_gn_8_124000' => 'lsa', 'Lsat_1_v5_gn_9_103081' => 'lsa', 'Manes.01G147700' => 'mes', 'Manes.02G106200' => 'mes', 'Manes.04G074700' => 'mes', 'Manes.16G108400' => 'mes', 'Mapoly0001s0550' => 'mpo', 'Mapoly0046s0014' => 'mpo', 'MBI04_g20309_MAGBIO' => 'mbi', 'MBI04_g20310_MAGBIO' => 'mbi', 'MBI04_g37500_MAGBIO' => 'mbi', 'MBI04_g37501_MAGBIO' => 'mbi', 'MBI04_g37502_MAGBIO' => 'mbi', 'MBI09_g42179_MAGBIO' => 'mbi', 'MBI09_g42183_MAGBIO' => 'mbi', 'MBI09_g42186_MAGBIO' => 'mbi', 'MBI12_g17646_MAGBIO' => 'mbi', 'MD02G1065400' => 'mdo', 'MD02G1128400' => 'mdo', 'MD10G1123700' => 'mdo', 'MD15G1196300' => 'mdo', 'MD15G1243600' => 'mdo', 'Medtr4g073530' => 'mtr', 'Medtr5g022450' => 'mtr', 'Medtr6g088680' => 'mtr', 'Medtr6g088685' => 'mtr', 'Medtr8g075350' => 'mtr', 'Medtr8g096220' => 'mtr', 'Medtr8g102510' => 'mtr', 'Medtr8g466670' => 'mtr', 'MELO3C013759.2' => 'cme', 'MELO3C020811.2' => 'cme', 'Migut.B00092' => 'egut', 'Migut.H02174' => 'egut', 'Migut.K00537' => 'egut', 'MSTRG.20002' => 'ama', 'MSTRG.23400' => 'ama', 'MSTRG.26384' => 'ama', 'Nitab4.5_0000566g0080' => 'nta', 'Nitab4.5_0000864g0200' => 'nta', 'Nitab4.5_0001658g0010' => 'nta', 'Nitab4.5_0001892g0010' => 'nta', 'Nitab4.5_0002337g0090' => 'nta', 'Nitab4.5_0005396g0010' => 'nta', 'Nitab4.5_0013387g0020' => 'nta', 'Nitab4.5_0022260g0010' => 'nta', 'Nn1g07875' => 'nnu', 'Nn5g30754' => 'nnu', 'Nn5g30755' => 'nnu', 'Nn5g30756' => 'nnu', 'Nn6g32359' => 'nnu', 'Nn6g35325' => 'nnu', 'Oeu014452.1' => 'oeu', 'Oeu014562.1' => 'oeu', 'Oeu019479.1' => 'oeu', 'Oeu064181.1' => 'oeu', 'Os01g0723100' => 'osa', 'Os03g0241900' => 'osa', 'Os06g0717100' => 'osa', 'Peaxi162Scf00328g00723' => 'pax', 'Peaxi162Scf00362g00848' => 'pax', 'Peaxi162Scf00439g00527' => 'pax', 'Peaxi162Scf00665g00339' => 'pax', 'PGR119G2113' => 'pgr', 'PGR142G1964' => 'pgr', 'PGR142G4262' => 'pgr', 'PGSC0003DMG400000297' => 'stu', 'PGSC0003DMG400003577' => 'stu', 'PGSC0003DMG400023880' => 'stu', 'PGSC0003DMG401006194' => 'stu', 'PGSC0003DMG401023899' => 'stu', 'PGSC0003DMG402006194' => 'stu', 'PGSC0003DMG402023899' => 'stu', 'Phvul.002G107200' => 'pvu', 'Phvul.002G308900' => 'pvu', 'Phvul.003G264500' => 'pvu', 'Phvul.004G014300' => 'pvu', 'Phvul.004G170500' => 'pvu', 'Phvul.011G034800' => 'pvu', 'Phvul.L001659' => 'pvu', 'Potri.004G174100' => 'ptr', 'Potri.005G111600' => 'ptr', 'Potri.006G164748' => 'ptr', 'Potri.009G133500' => 'ptr', 'Potri.018G087500' => 'ptr', 'Pp3c14_21370' => 'ppa', 'Pp3c14_6530' => 'ppa', 'Pp3c15_25770' => 'ppa', 'Pp3c18_22470' => 'ppa', 'Pp3c1_10660' => 'ppa', 'Pp3c22_6990' => 'ppa', 'Pp3c2_37270' => 'ppa', 'Pp3c3_16430' => 'ppa', 'Pp3c5_15770' => 'ppa', 'Pp3c6_8990' => 'ppa', 'Pp3c7_20760' => 'ppa', 'PRCOL_00005068' => 'pco', 'Prupe.7G170600' => 'ppe', 'Prupe.7G220100' => 'ppe', 'Prupe.8G164100' => 'ppe', 'Psat1g047160' => 'psa', 'Psat2g153480' => 'psa', 'Psat4g100960' => 'psa', 'Psat7g016960' => 'psa', 'Psat7g137680' => 'psa', 'PSO063G0128' => 'pso', 'PSO170G1801' => 'pso', 'PSO210G1731' => 'pso', 'PSO210G2822' => 'pso', 'PSO339G0777' => 'pso', 'PSO541G2811' => 'pso', 'PSO541G5243' => 'pso', 'PSO675G3461' => 'pso', 'PSO724G0430' => 'pso', 'PSO729G0009' => 'pso', 'PSO729G0086' => 'pso', 'PSO729G0207' => 'pso', 'PSO781G0054' => 'pso', 'QL02p041645' => 'qlo', 'QL02p041676' => 'qlo', 'QL04p094165' => 'qlo', 'QL06p050957' => 'qlo', 'QL06p050967' => 'qlo', 'QL11p049979' => 'qlo', 'QL11p049984' => 'qlo', 'RcHm_v2.0_Chr2g0091841' => 'rch', 'RcHm_v2.0_Chr2g0099181' => 'rch', 'RcHm_v2.0_Chr6g0252261' => 'rch', 'Rhsim03G0236800' => 'rsi', 'Rhsim10G0210700' => 'rsi', 'Rhsim11G0191500' => 'rsi', 'Sabra04G0115900' => 'sbr', 'Sabra05G0091300' => 'sbr', 'Sabra06G0126500' => 'sbr', 'Sabra06G0126600' => 'sbr', 'Sabra18G0075700' => 'sbr', 'Sabra18G0075800' => 'sbr', 'SalBow1G0216' => 'sbo', 'SalBow1G3959' => 'sbo', 'SalBow1G4414' => 'sbo', 'SalBow1G5873' => 'sbo', 'SalBow3G3763' => 'sbo', 'Sc07g0001060' => 'sci', 'Sc18g0001480' => 'sci', 'Sc18g0006500' => 'sci', 'Sed0008394' => 'sed', 'Sed0012153' => 'sed', 'Sed0013235' => 'sed', 'Sed0025841' => 'sed', 'SEGI_15472' => 'sgi', 'SEGI_17457' => 'sgi', 'SEGI_20717' => 'sgi', 'SEGI_25235' => 'sgi', 'SEGI_26193' => 'sgi', 'SEGI_26989' => 'sgi', 'SEGI_27374' => 'sgi', 'SEGI_30830' => 'sgi', 'SEGI_37346' => 'sgi', 'SGA_v2.0_scaffold58G20383' => 'sas', 'SGA_v2.0_scaffold78G25381' => 'sas', 'SHI02694' => 'shi', 'SHI08527' => 'shi', 'SHI51769' => 'shi', 'SHI51770' => 'shi', 'SHI53670' => 'shi', 'SHI54659' => 'shi', 'SHI55162' => 'shi', 'SHI55194' => 'shi', 'SMO196G0252' => 'smo', 'SMO200G0030' => 'smo', 'SMO364G0100' => 'smo', 'Solyc02g062050.3' => 'sly', 'Solyc02g062100.4' => 'sly', 'Solyc02g083690.2' => 'sly', 'Solyc12g008460.2' => 'sly', 'Sopen00g005930' => 'spe', 'Sopen01g053500' => 'spe', 'Sopen02g013050' => 'spe', 'Sopen02g028460' => 'spe', 'Sopen12g003410' => 'spe', 'Sp3g19620' => 'spa', 'Sp3g31290' => 'spa', 'Sp5g10970' => 'spa', 'Sp7g13670' => 'spa', 'Sp7g33755' => 'spa', 'Sp7g33760' => 'spa', 'SpUn1612_0010' => 'spa', 'TAR376G0393' => 'tar', 'TAR381G0415' => 'tar', 'TAR381G1730' => 'tar', 'TAR624G0650' => 'tar', 'THA.LOC104802547' => 'tha', 'THA.LOC104804269' => 'tha', 'THA.LOC104819174' => 'tha', 'THA.LOC104819745' => 'tha', 'Thecc.01G015800' => 'tca', 'Thecc.02G061700' => 'tca', 'Thecc.09G100900' => 'tca', 'Thhalv10010357m.g' => 'esa', 'Thhalv10020930m.g' => 'esa', 'Thhalv10022685m.g' => 'esa', 'Thhalv10025458m.g' => 'esa', 'Thhalv10027489m.g' => 'esa', 'TPR.G10516' => 'tpr', 'TPR.G19481' => 'tpr', 'TPR.G21374' => 'tpr', 'TPR.G23469' => 'tpr', 'TPR.G39196' => 'tpr', 'TWI53G0329' => 'twi', 'TWI63G0321' => 'twi', 'TWI79G0975' => 'twi', 'unitig_0.g824' => 'ugi', 'unitig_27.g25345' => 'ugi', 'unitig_899.g15432' => 'ugi', 'vmacro02271' => 'vma', 'vmacro06251' => 'vma', 'vmacro22144' => 'vma', 'VMungo0251G0792' => 'vmu', 'VMungo0251G0814' => 'vmu', 'VMungo0464G1422' => 'vmu', 'VMungo0540G0572' => 'vmu', 'VMungo1127G0447' => 'vmu', 'VMungo1215G1830' => 'vmu', 'Zm00001eb228160' => 'zma', 'Zm00001eb361690' => 'zma', 'Zm00001eb398940' => 'zma' ) $gf_id = 'HOM05D001259' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001259' ) $data_identifier = 'HOM05D001259' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 5, 'lsa' => (int) 14, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 5, 'ppa' => (int) 11, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 9, 'sas' => (int) 2, 'shi' => (int) 8, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 7, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398940' $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